Ophelia Violet is lovely.  Violet Ophelia works too, and Ophelia is not a filler middle!  For other less common floral names you might like that sound nice with Ophelia, I'll suggest Lilac, Marigold, Lavender and Amaryllis.

Ophelia Pepper is a lot of fun to say!  My hesitation with it is that it sounds a little character'ish.  Ophelia Pepper could be a fiesty girl detective or a character in Harry Potter perhaps.  Not bad things by any means, but maybe something to be aware of.  Names that have a similiar sound but are a little more mainstream...Piper, Poppy, Penelope, Pearl.  

Ophelia Opal is probably my favorite.  I love the family connection so much the O.O initials don't bother me at all. 

Of the three you've listed I think I like Ophelia Violet the best. Ophelia to me is a kind of strange name. I don't mean that in a bad way but in a "hard to classify" way. There is the literary connection of course. It is also a Greek name, a long name, and feels a bit flowery even though it is not a nature name. It also has a regal queen-like feel for me. Other names matching at least one of those characteristics for me are Aurelia, Caroline, Phoebe, Suzanne, Violet, and Miranda. Maybe you like some of them too and could mix and match for more options.

My other thoughts are on Opal. I like this name but it has a very different feel than Ophelia. It is shorter for one. More country than regal, but is super pretty being a gem name. What is the baby's birth gem? If it is something workable than maybe use that as a middle.

Ophelia Ruby; Miranda Opal; Aurelia Suzanne; Phoebe Caroline=just some other combos for you to think on but I don't think any of your list is a bad choice either.

I really like Ophelia.  It's pretty, recognizable and not over the top.  I think Ophelia Violet sounds the best.  Ophelia Pepper could definitely work, but I think it would depend on your last name.  If you last name is somewhat simple and "smooth" (can't remember the real terms for soft sounds versus hard consanonts) - it would work.  For example I think Ophelia Pepper Smith or Zazi sounds good, but Ophelia Pepper Tannenbaum or Martinez is too long and too choppy.

Ophelia Opal ... I have mixed thoughts on it... I don't so much mind the double O's, but I don't really like the way it looks in that Opal has all the same letters as Ophelia.  It's interesting cause I think it sounds fine!  So if that doesn't bother you than I'd say go for it.

I love Ophelia Pepper, and it gives her the option of going by Pepper if she wants to.  Ophelia Violet is lovely, but the names have such similar style that it almost feels a bit bland.  Still, no reason not to use it if you love it.  Ophelia Opal is pretty too.  I don't think the double-O would worry me unless your last initial makes it problematic.

A lot depends on the family name that's going to get added at the end of any of these, but here are my thoughts.

I would love to meet a little girl named Ophelia. It's such a wonderfully literate name, if you know what I mean.

Ophelia Violet: this sounds like you mis-remembered your Shakespeare. (The character in Twelfth Night is Viola.) On the plus side, it gives her a more "mainstream" fallback if for some reason she doesn't like Ophelia. And I don't think Violet is quite at the level of "filler" middle name yet.

Ophelia Pepper: wow, that'd be a fun character in a novel! Not much of a mainstream fallback, but if you love it, use it.

Ophelia Opal: it sounds like you have the most personal connection with this one. Again, not much of a fallback, but I think it works fine sound-wise, and unless your surname also starts with O, I don't think the initials should be a problem. (Well, maybe I'd avoid OOF. But OOH would be fun.)

Ophelia and J0nah would be an interesting pairing: a traditional -a feminine ending paired with one of the few clearly masculine names that ends in that sound. Makes me wonder: are there any clearly feminine names that end with the traditional Latin masculine -us? (The closest I can think of offhand are Agnes and Ruth...)

I like the way Ophelia sounds, and if you and your husband aren't too concerned with Hamlet's Ophelia's ill-fate, I think your baby will have a lovely name.  I think Ophelia Violet sounds the best to me.  We come from a generation of filler middle names but I don't think that's the modern trend.  At least from the babies I know, their middle names are chosen with as much care as their firsts.   Currently Violet sits at #184, which is still uncommon (well depending on your community). 

As far as cultural implications: Ophelia mentions violets in her mad bouquet picking song before she dies-- she says she has daisies because all the violets died when her father did.  Ophelia as a character and name has culturally been associated with gothic and macabre themes.  Especially when paired with Violet (nn "vile"), Ophelia Violet has a lot of darker themes for me, besides being a pretty name for a pretty girl. 

Both Ophelia and Violet fall in the dark themed catagory for me, (like Raven, Delilah, Jezebel, Desdemona, and Lilith, off the top of my head).  I don't think there's anything wrong with the name at all, it's very pretty sounding.  I did a quick search of "gothic baby names" to make sure I am not the only one who thinks that way and Ophelia makes the list for many of them, although Violet doesn't.  I read a book once with a protagonist named Vile (short for Violet) so I think the association lingers for me.

As for your other choices, an O. O. initial will make it very hard for her to get anything monogrammed (I am an EYE myself) and I don't like Pepper nearly as much as Violet.

I happen to like Ophelia and have known an Ophelia, an Ofelia and an Ofelie (accent on the 1st e) at different points in time (they range in age from mid 20s to late 50s). Ophelia is pretty and frilly without being cloying, a nice alternative to Olivia and the Shakespeare connection doesn't bother you, which is usually the turn off. (Which is a shame that Mr. Shakespeare gave some lovely names longterm negative associations.) I'd go for it.

For me Opal and Violet work the best. The double O doesn't bother me so much (I like the connection), but I can imagine yelling Ophelia Violet across a playground better than Ophelia Opal. Pepper is an offbeat choice, but probably best in the middle name slot. If you both love it, go for.

It feels like either a 1- or 3-syllable middle name might work better than a 2-syllable combo, so other names that might work:Adeline (ada-line or ada-leen), Beatrice, Augusta, Rosalie, Felicity, Miranda, Johanna (though that might be too close to Jonah), Aurelie, Rosalind, Anne, Jane, Grace (though that might feel like a filler for you).

Good luck.

My choices would be Ophelia Violet or Ophelia Pepper. Pepper is unusual and perhaps better on a child than an adult, but the beauty of a middle name is that she can shorten it to a middle initial if it becomes inconvenient. I like how it balances out the weightiness of Ophelia. I love Violet, I think it sounds great with Ophelia, and wouldn't consider it a filler middle name. Esther E. has raised some interesting points about how Ophelia and Violet add up to a darker theme —that's another angle to consider, though I think it's safe to say that the vast majority of people won't make that connection. Ophelia Violet is more elegant, sophisticated and feminine; Ophelia Pepper is bold and spunky. Between the two, I might wait to meet the baby and then decide.

I'm not as big a fan of Ophelia Opal. The double O doesn't bother me so much as the way the vowels between the names run together (-ia O-). I prefer -ia names to be followed by a strong consonant. I also don't care for the visual impact of the repeated Op-l, as a poster above mentioned. They're both lovely names, I just don't love the combo. 

While I don't love the combo of Ophelia and Opal for all the reasons that have already been mentioned, it occurs to me for the first time that Opal might actually be a really great nickname for Ophelia -- a name that I like a lot, but have always thought had the disadvantage of having no cute diminutives for something so long.  (I mean, you can hardly call a kid Feelie, right?) 

For a middle, I would pick Violet, which I think matches beautifully and doesn't feel "filler" to me at all.  I don't find the Shakespearean connotations overwhelming, just kind of cool.  Ophelia Pepper could grow on me, but the styles are so very different that I find it a little jarring on the first encounter.

Since nobody has mentioned it yet, I will just chime in to say that my biggest hesitation with Ophelia is probably not the Shakespeare thing (which is a concern, but surmountable, I think), but the "Oh feel ya" sound, which makes it seem like it could be subject to dirty jokes, or at least something silly and punny (like a reply to "ya feel me?" "yeah, I feel ya (Ophelia)").  Of course, all names/people are open to teasing for something or other, but the sound of this is prominent enough that it gives me some pause.  Other than that, though, I do think it is a pretty name, and I like all of your MNs with it.  I personally prefer either Violet or Opal, because I think both are beautiful and sound great with Ophelia (the O.O. thing does not bother me), but Pepper is spunky and interesting for a MN--it wouldn't be my choice, but I would definitely appreciate it on someone else's kid.    

p.s. If you are considering any alternatives to Ophelia, have you thought about Olympia, Octavia, Odette, or Odessa?  I think they are all pretty cool and stylish. 

I like Ophelia Violet best and don't think of Violet as a filler name at all. Ophelia Opal has a nice family connection but I don't like how they sound together too much. Not a fan of Ophelia Pepper.

I love the Shakespeare connection, even if Shakespeare's Ophelia did not have a happy end.

Jonah and Ophelia seem very different to me. This may not be an issue for you.  I personally do not care for it.  Too frilly and almost ornate sounding.  Although it is highly unusual (never met one), in this day and time there are so many unusual names floating around that most people wouldn't bat an eye.  It has a similar sound to the uber popular Olivia. Very Shakespearan.  The only combo I like is Ophelia Violet. Ophelia and Pepper are so stylistically dissimilar it feels like a pairing of two completely unrelated names which just doesn't work for me personally.  I don't even care for the flow when it is said. Ophelia Opal does not flow at all to my ears. 

I love Ophelia and would love to see someone use it.

Yes, it has the negative Shakespearean character association and the 'oh feel ya' potential for teasing but I don't think either of those are deal breakers.

Of your combos I like Ophelia Violet the best. Ophelia Pepper doesn't work for me, it sounds too fantasy or jokey?  Ophelia Opal doesn't bother me for the initials but the sounds are too similar. I also had the thought that Opal could be the nn for Ophelia.

Some combos I thought of:

Ophelia Pearl (same sytle to Opal but different sounds)

Ophelia Wren 

Opehlia Piper (instead of Pepper?)

Ophelia Lark

Ophelia Ruby

Ophelia Mae

I like Ophelia Pepper and Ophelia Opal (fun/unexpected/personal) a lot more than Ophelia Violet. I guess I do see Violet as a bit of a non-exciting filler for reasons I can't really explain. It sounds like your secret fave is Pepper but you hesitate to use it as a first name, and I think it's a great solution/compromise to use it as a middle name. Plus, I notice how you like Opal for a specific reason while you "just" like the name Violet (but dislike its popularity)... Basically, given these three combos - which are far from outrageously bizarre - I'd say choose the one you love the most!

Ophelia Opal is perfect.

It sounds beautiful and you have a great connection with the name.
My first and middle names alliterate and I love it! I don't really use my middle name but I love the romantic sound of the two names together, especially because both are very vowel-heavy. All the letters of my sister's middle name appear in her first name, too, but she just thinks it's cool. Hence I don't think any of the issues with the pairing that have been raised are a cause for concern.

I can't think of any combo that is as harmonised. 

I really like Ophelia - but I do have a soft spot for 'accessible' Greek names. I really like the Ophelia Violet combo. I personally do not like to use popular names as first names but I use the middle spot to use the names that I love which are becoming too popular. That seems to be your problem with Violet but I see no problem when it's in the middle. Also, it's not a filler name like Rose yet, as others have said.

Also loved someone's suggestion of Opal as a nickname for Ophelia because I do find that combo a bit much personally.